The EU nitrogen expert panel (EUNEP) has proposed nitrogen-based indicators for farm productivity (N output), efficiency (NUE) and environmental emissions (N surplus). This model-based study (using the Daisy model) was carried out, i) to study the effects of soil type, soil organic matter (SOM), cropping pre-histories varying in C input, 3-to-4 manure-to-mineral N proportions and ten crop rotations on the N-based indicators, and ii) to evaluate the adequacy of these indicators by establishing quantitative relationships between N surplus, N loss and soil organic N (SON) stock change. The results, averaged over 24-year simulation period, indicated that grass-clover dominant rotations had highest N output and showed a tendency to increase SON stocks when compared with spring-cereal monocultures. For most rotations, the NUE ranged between 70 and 75 %. The SON stocks were mainly influenced by initial SOM and cropping prehistory, and stocks increased only under low initial SOM and low C input cropping pre-history (spring barley). Overall, SON stocks tended to increase under low C input pre-history, coarse sand, low initial SOM and high manure N, however, this combination did not result in highest productivity, NUE, and lowest N losses. The relations between N surplus, N loss and SON stock change were strongly affected by crop rotations, emphasizing that using N surplus as an indicator for N leaching/losses while ignoring changes in SON stocks may result in biased conclusions, e.g. estimated average error for N losses ranged from −45 % (underestimation) for maize monoculture to +50 % (overestimation) for continuous grass-clover ley. The results also imply that the environmental assessment of cropping systems must be improved by combining above indicators with estimation of N loss and SON stock changes. This study provides a detailed account of N balance components/N indicators for diverse crop rotations and their use according to the recommendations of the EUNEP.